Leftovers
by ThatKyubiBrat
Summary: Sometimes, when something breaks, you need a backup. However, not everything is backwards compatible.
1. Chapter 1

Chapter One: An Introduction to a Problem.

Shinji was in pain. Grievous pain, though understandable considering the circumstances. After all, it wasn't everyday a teenage boy pilots a giant robotic… thing, to fight an equally large alien thing, without a shred of experience, and wins.

Not as if it would happen again, as it is quite difficult for a boy to pilot anything if he is not a boy. By definition it was impossible, and confusing, very confusing. Details shall be provided later in this archive, which documents the actions of the members involved in this incident. However, it is important to explain that this "boy" was the only hope left for the entire organization, also known as NERV, and what a slim hope he/she was. Commander's "son" or not, the actions inscribed here can only be described as inconceivable.

It was such a shame that he/she had to suffer so much.

Anyway, let us begin.

_[These details were obtained through rather… questionably methods, which means that they are accurate, so no problem with unreliable narrators, or at least, not yet.]_

Gendo was nervous. He told himself that he shouldn't be, after all it was only his son. To his immense surprise, the boy did put up a fantastic fight. It wasn't supposed to go like that, not in his plans. The fact remains, the third angel, Sachiel, was dead, and humanity wasn't.

His eyes trailed over the broken body that used to house his son's soul. The boy had been extracted from the Eva as soon as possible, and even when he was set into the emergency room, he was fine, beyond a few cuts and scrapes. It was only when he opened his eyes and saw his father, did his heart rate flat line.

His last words were "Tou…san."

Gendo didn't know whether he should be insulted, or impressed by the well done death scene.

Anyway, he couldn't have the boy dying on them; it would be disastrous to morale, and, while he disliked mentally saying it, they didn't have any other options. Even when Rei recovered, she didn't display nearly the skill Shinji did, and it wasn't good to hope for a miracle right after you got one.

Then he had an idea; a really stupid one, but an idea nonetheless. He whispered this plan into the ear of one Dr. Akagi, which made her eyes widen in shock.

"Commander, you can't be serious!" she all but shouted. Gendo gave her patented 'Gendo Glare' in response.

"I am always serious; now fetch the body while no one is looking." And with that, she did as he said.

Three people left the room at that moment, and only two were living.

Shinji groaned as he opened his eyes. He felt like his body had been compressed so much that it imploded. That was, until he started to really pay attention to reality, as opposed to what his brain had been telling his to feel. When he did that, he realized that he actually wasn't in pain. In fact, he felt… fresh? No, that wasn't the right word, but that didn't matter right now.

His vision cleared, and for the first time in all his years, he could truly see.

His previous guardians always told him that he needed glasses, but he adamantly refused all offers of the face accessory. Shinji was already Gendo's son; he didn't need any sort of similarities between them. That is also why for a brief period in his life, he had long blonde hair, which is guardians immediately chopped off.

But now, Holy Crap!

Everything was sharper, so much more defined. Hell, he could even read the text on the far side of the room, something impossible before now. He could see Dr. Akagi and his father, along with all the hospital instruments.

Wait a second, what?

Shinji's eyes swiveled in order to get a glance at his father. Gendo was in his 'Scheming Pose', with his hands folded in front of his face; obscuring his mouth. He could see that his father's once white gloves were now stained with blood. The feeling of his stomach turning inside out was obvious once he figured it out.

'_That's my blood.' _

Shinji felt like fainting, or at least yelling at his father, but he couldn't muster the strength. Rather, the only thing that he could spit out (though at least it wasn't his lunch) was a flaccid and childish, "Father?"

His voice seemed to be a bit different from before, but that was hardly the issue.

The commander spoke loudly and clearly, further proving to Shinji how different the two of them really were. "Your body was injured. We tried fixed you using an experimental procedure. It worked. Dr. Akagi will brief you on your schedule." With that, Shinji's father walked out, intent on leaving all the troublesome explaining to Ritsuko.

'_Just like always.'_ Shinji thought bitterly, _'Whenever he no longer needs me, he sets me aside. Why? I defeated the Angel you bastard! You _need_ me. If I didn't show up you would all be dead. Even her…' _Shinji shook his head bitterly, failing to notice how his hair whipped around him.

In spite of his attempts to not show weakness, his eyes begun to sting (fortunately he did _not_ cry, proving his father wrong about one thing). This brought attention to his own body, which had been ignored with all the family issues that plagued the young boy's mind. He raised his hand to wipe the non‐existent tears from his face. While he didn't know why his eyes hurt, he did notice a now slightly blurry hand that was not his own in front of his face. The pain dulled as he now curiously examined the foreign appendage.

It was a small hand, at least compared to his. It had smooth, slightly pale skin, a color that reminded him of something, but for the life of him he couldn't remember.

Shinji commanded his own hand to close, and the feminine hand before him followed his orders.

A few seconds of processing passed, before it really hit him. The young teenager (as boy was no longer the correct word to use) forced himself up. Things, which were attached to his chest, bounced wildly. He looked at Dr. Akagi, who was taking everything rather well, and asked, "What the hell is going on?" His voice was now most definitely different, and the difference was making way to much sense. He could only hope that the doctor would prove him wrong.

She calmly cleared her throat and said, "The procedure had the… undesired effect of changing your genetic code, more specifically, the Y chromosome, which has clearly been turned into an X chromosome. I'm sorry, Shinji‐kun."

Shinji then did the most feminine thing he could think of, and fainted.


	2. Chapter 2

Leftovers Chapter 2

_It is important to note the significance of some of Shinji's actions. While in due time, conclusions about why he did certain things could be made, assuming is an unreliable art. That is why, in order to best present this archive, we have gotten the subject, Shinji, to go over the event from his point of view. However, at times it will be necessary for other insertions to be made. Readers will be forewarned._

Staying in the hospital was a… challenge at best, and torture at most accurate. It was a while before I was even allowed to leave, but I'm getting ahead of myself. Ritsuko did every possible test she could think of, all of which confirmed what she already knew. I had to leave eventually; after all possible tests were exhausted. I did not have cancer, or brain damage (Which Dr. Akagi said she was most worried about, but refused to tell me why), or any STD's (which she was also concerned about, and that quite frankly freaked me out). All in all, besides a minor headache, I felt fine; ignoring the whole 'I'm a girl' thing of course.

Anyway, when the time for my departure, came around, so did another person. When I heard the knocking, I thought for a second that it might be Misato, as she was the only person who would have bothered to visit me. Then I realized that Misato would just burst in, not caring about the consequences. It turned out to be a soul I hadn't seen since my fight with the first angel.

Ayanami Rei, fellow Eva pilot and current cripple. Apparently, the higher ups decided that the only way for me to cope with this was to get an actual school girl to help me. And look! They happened to have one, all ready to teach, and with plenty of time to spare. It makes me sick.

Of course, at the time I did not know that, so I continued to puzzle her arrival. It did mean one thing, I still had a use. And as long as I had a use, I could prove to Father that leaving me was a mistake.

_I will show him_

Moving my thoughts back to the task at hand, Rei. Somehow, in the time I spent musing, she had thrown an article of clothing on the bed. My eyes focused, while I internally smiled at their increased performance. I blanched at what I saw.

It was a plug suit.

More specifically, it was Rei's suit, and I'm pretty sure she wasn't waiting for me to leave so she could change.

I dumbly pointed to it and asked, "You want me to…?" She gave a short, curt nod. I sensitively raised myself form my bed and stood before the blue haired girl. My face was flushed as I said, "Ano…"

Her blank stare seemed to ask me, "What is it?" in the way a person would talk to a dog they don't have the patience for, but maybe that was just my imagination.

Never the less I was able to mutter out, "Changing in front of a girl…" Her stare, which had not physically changed, now just said, "You're an idiot."

Rei stepped forward, and how she did this will always be a mystery for me, removed my hospital gown in a single movement. So now I was naked, in front of a rather attractive girl, who was currently staring at my (though not by my choice) feminine body with a quizzical expression on her face. My shock at her face actually expressing an emotion besides pain seemed to counteract my self-consciousness enough for me to actually squeak something out.

"What is it?" She shook her head.

"It is nothing, now if you would please continue…" she gestured to the plug suit. If I didn't know any better, I would say that she was enjoying this.

I grabbed the suit. Rei had to help me slid it on, as I was definitely not used it as a guy, much less a girl.

I tried, oh great Ameterasu I tried, to not think about Rei's smooth, lithe, naked body, sweating feverishly in the suit.

Oh yeah, I was doing a great job of that. I shook my head to clear my thoughts.

Once the baggy suit was on, Rei pressed a button on the wrist (The other plug suit I had worn had the button on the chest). It contracted until it was skin tight, and showing every damn curve I desperately wanted to believe I didn't have.

If I was flushed before, now I was the color of the reddest tomato in the universe. My breasts were compressed, not painfully, but enough that I couldn't stop noticing it. Needless to say, that was uncomfortable. Not to mention my lower body; which was awkward at best.

Rei turned me around, so that I was facing a full length mirror that I didn't know existed, most likely because it was just out of sight from the bed I had been confined to for Ameterasu knows how long. I was stunned at what I saw.

The resemblance between me and Rei was uncanny. If I didn't know better, I said say that we were sisters, if not twins! Our faces were virtually identical, as was our generic body shape. Our height was the same as well, though that was the least surprising, after all I was never know for my height. I only noticed a few slight differences. I was a bit tanner, but for all I know that was a result of being under surgical lights for so long, and even so, the difference wasn't that obvious. The major difference was our hair color (Mine being a nice brown, exactly the same as when I was a boy). Just color though, length and style were exactly the same. I guess that one could say that mine was a bit shaggier; however I didn't have any time to go over my appearance, while she had… I don't know how much free time she had, but I had to assume it was more than me.

For some reason, I was reminded of my mother. I suppose it makes sense that girl me looked like her, but why did Rei? I would assume that Gendo had cheated on her, before I realized that it was her genes that would have to be passed down. And it wasn't likely that Mom would cheat on Gendo, despite how much any sane person would want to. Mom is better than that, better than Him. The whole thing made me uncomfortable, so I swiftly moved those thoughts out of my mind.

My eyes were the same as always, which was my only source of comfort in all of this. They say that eyes are windows to the soul, which means my soul is existent and present, in a modified container perhaps, but alive.

I am Shinji Ikari, and I am still alive.


End file.
